Collect and apply field maps #79
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## main #79 +/- ##
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- Coverage 30.83% 30.79% -0.04%
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Files 26 27 +1
Lines 2374 2416 +42
Branches 289 294 +5
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+ Hits 732 744 +12
- Misses 1619 1648 +29
- Partials 23 24 +1 ☔ View full report in Codecov by Sentry. |
src/fmripost_aroma/workflows/base.py
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| # Warp desc-preproc_fieldmap to boldref space | ||
| # Warp the mask as well | ||
| fieldmap_to_boldref = pe.Node( | ||
| ApplyTransforms(), | ||
| name='fieldmap_to_boldref', | ||
| ) |
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This node needs to go into the bold_MNI6_wf because you want to resample from fmap to the MNI space.
| distortion_params = pe.Node( | ||
| DistortionParameters(metadata=metadata), | ||
| name='distortion_params', | ||
| run_without_submitting=True, | ||
| ) | ||
| workflow.connect([ | ||
| (inputnode, fmap_select, [ | ||
| ('fmap', 'fmap_ref'), | ||
| ('fmap_id', 'keys'), | ||
| ]), | ||
| (inputnode, distortion_params, [('bold_file', 'in_file')]), | ||
| # Inject fieldmap correction into resample node | ||
| (fmap_select, resample, [('fmap', 'fieldmap')]), | ||
| (distortion_params, resample, [ | ||
| ('readout_time', 'ro_time'), | ||
| ('pe_direction', 'pe_dir'), | ||
| ]), | ||
| ]) # fmt:skip |
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Here is the section where you need to resample the fieldmap from fmap space to target space, using the inverse boldref2fmap transform, in addition to the boldref2anat and anat2MNI transforms. Then you pass in the fieldmap in MNI space to resample.
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
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@effigies thanks for intervening directly on this. I started addressing your review last weekend but got drawn into other things. I'm hoping to test out the changes here soon. |
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@tsalo is this working for you? I need to implement it in fMRIPrep... |
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I haven't had a chance to try it yet. I might be able to give it a try by the end of the week though. |
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Well, I'll implement it over in fMRIPrep and we'll see how I do. Thanks for laying the groundwork! |
Closes #63. Once this is working, I'll copy over the changes to
fmripost_template.Changes proposed in this pull request